PosMed-plus: An Intelligent Search Engine that Inferentially Integrates Cross-Species Information Resources for Molecular Breeding of Plants
PosMed-plus: An Intelligent Search Engine that Inferentially Integrates Cross-Species Information Resources for Molecular Breeding of Plants
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DOI：
10.1093/pcp/pcp086
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发表时间：
2009-07-01
影响因子：
4.9
通讯作者：
Toyoda, Tetsuro
中科院分区：
文献类型：
--
作者：
Makita, Yuko;Kobayashi, Norio;Toyoda, Tetsuro
作物分子育种是提高植物功能的有效途径。关键的一步是正向遗传学或定位克隆，以确定赋予有用功能的基因。为了加快整个研究过程，我们开发了一个集成的数据库系统，由一个智能数据检索引擎，称为PosMed-plus（植物升级科学的定位Medline），使我们能够优先考虑高度有前途的候选基因在一个给定的染色体间隔（S）的拟南芥和水稻，水稻。通过整合跨物种的信息资源，包括基因组，转录组，蛋白质组，定位组，表型和文献，系统比较用户的查询，如表型或功能的关键字，与相关的基因位于区间内的文献。通过利用直系同源和旁系同源的对应关系，PosMed-plus有效地整合了跨物种的信息，以促进水稻候选基因的排名基于其他模式物种，如拟南芥的证据。PosMed-plus是被哺乳动物研究人员广泛使用的PosMed系统的植物科学版本，并提供了强大的综合搜索功能和丰富的综合显示的综合数据库。PosMed-plus是第一个跨物种的综合数据库，它为植物科学中的正向遗传学方法确定了候选基因的优先顺序，并将在许多物种的植物升级中得到更广泛的使用。
Molecular breeding of crops is an efficient way to upgrade plant functions useful to mankind. A key step is forward genetics or positional cloning to identify the genes that confer useful functions. In order to accelerate the whole research process, we have developed an integrated database system powered by an intelligent data-retrieval engine termed PosMed-plus (Positional Medline for plant upgrading science), allowing us to prioritize highly promising candidate genes in a given chromosomal interval(s) of Arabidopsis thaliana and rice, Oryza sativa. By inferentially integrating cross-species information resources including genomes, transcriptomes, proteomes, localizomes, phenomes and literature, the system compares a users query, such as phenotypic or functional keywords, with the literature associated with the relevant genes located within the interval. By utilizing orthologous and paralogous correspondences, PosMed-plus efficiently integrates cross-species information to facilitate the ranking of rice candidate genes based on evidence from other model species such as Arabidopsis. PosMed-plus is a plant science version of the PosMed system widely used by mammalian researchers, and provides both a powerful integrative search function and a rich integrative display of the integrated databases. PosMed-plus is the first cross-species integrated database that inferentially prioritizes candidate genes for forward genetics approaches in plant science, and will be expanded for wider use in plant upgrading in many species.